mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 125,387 | C→T | 100% | Q791* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 475,971 | C→G | 14.4% | intergenic (+20/+11) | ybaY → / ← atl | PF09619 family lipoprotein YbaY/DNA base‑flipping protein |
| RA | 475,972 | C→G | 14.4% | intergenic (+21/+10) | ybaY → / ← atl | PF09619 family lipoprotein YbaY/DNA base‑flipping protein |
| RA | 569,160 | G→T | 5.2% | D87Y (GAC→TAC) ‡ | ybcK → | DLP12 prophage; putative recombinase |
| RA | 569,161 | A→C | 5.0% | D87A (GAC→GCC) ‡ | ybcK → | DLP12 prophage; putative recombinase |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 709,461 | C→T | 9.2% | G376G (GGC→GGT) | chiP → | chitobiose outer membrane channel |
| RA | 710,595 | G→T | 100% | P18T (CCT→ACT) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 759,250 | G→T | 100% | R182L (CGC→CTC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 800,807 | G→T | 100% | A17S (GCG→TCG) | ybhH → | putative isomerase YbhH |
| RA | 1,166,293 | C→T | 100% | A70V (GCC→GTC) | ndh → | NADH:quinone oxidoreductase II |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,388,283 | C→T | 14.8% | intergenic (+22/+22) | tyrR → / ← tpx | DNA‑binding transcriptional dual regulator TyrR/lipid hydroperoxide peroxidase |
| RA | 1,388,284 | A→T | 14.7% | intergenic (+23/+21) | tyrR → / ← tpx | DNA‑binding transcriptional dual regulator TyrR/lipid hydroperoxide peroxidase |
| RA | 1,388,285 | A→G | 17.3% | intergenic (+24/+20) | tyrR → / ← tpx | DNA‑binding transcriptional dual regulator TyrR/lipid hydroperoxide peroxidase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| JC | 2,392,615 | Δ3 bp | 100% | coding (425‑427/1530 nt) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,484,369 | A→G | 10.2% | *205* (TAA→TAG) | evgA → | DNA‑binding transcriptional activator EvgA |
| RA | 2,568,146 | G→A | 11.7% | intergenic (‑39/+178) | eutH ← / ← eutG | putative inner membrane protein/putative alcohol dehydrogenase in ethanolamine utilization |
| RA | 2,568,147 | C→A | 13.3% | intergenic (‑40/+177) | eutH ← / ← eutG | putative inner membrane protein/putative alcohol dehydrogenase in ethanolamine utilization |
| RA | 2,568,153 | A→T | 11.4% | intergenic (‑46/+171) | eutH ← / ← eutG | putative inner membrane protein/putative alcohol dehydrogenase in ethanolamine utilization |
| RA | 2,568,154 | A→T | 13.7% | intergenic (‑47/+170) | eutH ← / ← eutG | putative inner membrane protein/putative alcohol dehydrogenase in ethanolamine utilization |
| RA | 2,568,160 | T→G | 11.2% | intergenic (‑53/+164) | eutH ← / ← eutG | putative inner membrane protein/putative alcohol dehydrogenase in ethanolamine utilization |
| RA | 2,568,161 | T→C | 13.0% | intergenic (‑54/+163) | eutH ← / ← eutG | putative inner membrane protein/putative alcohol dehydrogenase in ethanolamine utilization |
| RA | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,761,623 | C→A | 9.4% | V640L (GTA→TTA) | abpB ← | CP4‑57 prophage; putative helicase YfjK |
| RA | 2,778,123 | G→T | 13.0% | intergenic (+341/+23) | ypjF → / ← ypjA | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| RA | 2,778,124 | A→C | 12.5% | intergenic (+342/+22) | ypjF → / ← ypjA | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,380,208 | G→A | 13.3% | A6A (GCG→GCA) | yhcB → | conserved protein YhcB |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,602,701 | T→C | 27.5% | Q16R (CAG→CGG) | ftsE ← | cell division protein FtsE |
| RA | 3,637,645:1 | +T | 100% | coding (4/1500 nt) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,719,876 | C→A | 81.9% | intergenic (+108/‑173) | yiaG → / → cspA | putative DNA‑binding transcriptional regulator YiaG/cold shock protein CspA |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,886,756 | G→A | 8.1% | intergenic (+34/‑72) | yidC → / → mnmE | membrane protein insertase YidC/5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| RA | 3,886,757 | T→C | 9.0% | intergenic (+35/‑71) | yidC → / → mnmE | membrane protein insertase YidC/5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| RA | 3,900,410 | A→T | 9.6% | P56P (CCT→CCA) | yieL ← | putative hydrolase YieL |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,114,431 | G→A | 100% | N14N (AAC→AAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,123,110 | G→A | 100% | P77L (CCA→CTA) | ftsN ← | cell division protein FtsN |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 19.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423753–3424530 | 3424530 | 1–778 | 11 [10] | [10] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 86076 | 29 (0.890) | 3 (0.100) | 3/256 | NT | 9.7% | coding (447/1725 nt) | ilvI | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| ? | NC_000913 | = 86085 | 28 (0.890) | coding (456/1725 nt) | ilvI | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit | |||||
| * | ? | NC_000913 | 167280 = | NA (NA) | 3 (0.100) | 3/242 | NT | NA | intergenic (+16/‑204) | mrcB/fhuA | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB/ferrichrome outer membrane transporter/phage receptor |
| ? | NC_000913 | 167307 = | NA (NA) | intergenic (+43/‑177) | mrcB/fhuA | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB/ferrichrome outer membrane transporter/phage receptor | |||||
| * | ? | NC_000913 | = 315572 | NA (NA) | 4 (0.130) | 4/244 | NT | NA | noncoding (344/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315588 | NA (NA) | noncoding (360/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 316093 | NA (NA) | 3 (0.090) | 3/258 | NT | NA | noncoding (865/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316135 | NA (NA) | noncoding (907/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 1300 (40.230) | 242/262 | NT | 98.1% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 26 (0.800) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 745824 = | 27 (0.830) | 3 (0.100) | 3/254 | NT | 10.5% | coding (660/735 nt) | pxpA | 5‑oxoprolinase component A |
| ? | NC_000913 | 745854 = | 25 (0.800) | coding (690/735 nt) | pxpA | 5‑oxoprolinase component A | |||||
| * | ? | NC_000913 | 1207790 = | 20 (0.610) | 12 (0.420) | 12/232 | NT | 39.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 19 (0.660) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 18 (0.550) | 12 (0.420) | 11/232 | NT | 40.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 19 (0.660) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1417458 = | 25 (0.770) | 3 (0.100) | 3/244 | NT | 12.2% | intergenic (‑72/+30) | recE/racC | Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific/Rac prophage; protein RacC |
| ? | NC_000913 | 1417483 = | 20 (0.660) | intergenic (‑97/+5) | recE/racC | Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific/Rac prophage; protein RacC | |||||
| * | ? | NC_000913 | 4189862 = | 30 (0.920) | 3 (0.100) | 3/254 | NT | 9.5% | coding (77/540 nt) | yjaZ | conserved protein YjaZ |
| ? | NC_000913 | 4189894 = | 28 (0.890) | coding (109/540 nt) | yjaZ | conserved protein YjaZ | |||||
| * | ? | NC_000913 | = 4470450 | NA (NA) | 4 (0.130) | 3/250 | NT | NA | noncoding (20/29 nt) | other | REPv339b |
| ? | NC_000913 | = 4470461 | NA (NA) | noncoding (9/29 nt) | other | REPv339b | |||||